VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Dec 07 2021 - 08:06:11 CST

Hi Kiana,
Where in the topology file is that dihedral showing up? Perhaps I missed it
but I didn't see any definition of it. How are you building your psf? Can
you post your script? You might need to explicitly add "auto none" to the
segment block for the iron-sulfur cluster.
Best,
Peter

On Tue, Dec 7, 2021 at 6:30 AM Kiana Jahani <kiana.jahani_at_yahoo.com> wrote:

> Dear Peter
> Yes, the error is "unable to find dihedral parameters for FEJO SJO FEJO
> SJO". I think you mean by using the term "auto angles dihedrals" in the
> script, all possible dihedrals will be generated. Actually I tried both,
> with and without this term, but the result didn't change.
> The topology file defines this dihedral but it isn't contained in the
> parameter file. Do you think the problem can not be solved (by this
> parameter file)?
> Best,
> Kiana
>
>
> On Monday, December 6, 2021, 05:27:19 PM GMT+3:30, Peter Freddolino <
> petefred_at_umich.edu> wrote:
>
>
> Dear Kiana,
> Are you sure that there is supposed to be a 'FEJO-SJO-FEJO-SJO' dihedral
> term? It does not appear in the parameter file, and it looks like the
> topology likewise does not define Fe-S-Fe-S dihedrals, so I suspect that
> you want to AVOID using automatic dihedral generation for this chain. Using
> AUTO DIHE will generate all possible dihedrals for atoms with the
> appropriate bonding pattern, but it looks like such dihedrals are not
> intended in this force field for the iron-sulfur cluster.
> Best,
> Peter
>
> On Mon, Dec 6, 2021 at 3:20 AM Kiana Jahani <kiana.jahani_at_yahoo.com>
> wrote:
>
> Dear Peter,
> Thank you so much for your reply. I used the topology and parameter files
> from the supporting information of the related reference "
> https://urldefense.com/v3/__https://pubs.acs.org/doi/abs/10.1021/ct800342w__;!!DZ3fjg!v7RiMBjlKWvvElEAMeJzxTDEExBYx-xwV89Hfs1X80WZPuBeKxE7NBGPdPALwSKLRQ$ ". (ct800342w_si_002.txt
> and ct800342w_si_003.txt files).
> The previous error was for F4O cluster. Actually I got the same error for
> F4R and FHO clusters.
> Best,
> Kiana
>
>
> On Sunday, December 5, 2021, 08:43:36 PM GMT+3:30, Peter Freddolino <
> petefred_at_umich.edu> wrote:
>
>
> What parameter files are you including, and what topology files did you
> use in building the iron sulfur cluster? Most likely you don't have the
> parameter file included that would contain the parameters for this cluster.
> Best, Peter
>
> On Sun, Dec 5, 2021 at 8:25 AM Kiana Jahani <kiana.jahani_at_remove_yahoo.com>
> wrote:
>
> Dear VMD Users
>
> I generated the psf file from a pdb file using psfgen. For minimization, I
> got the following error:
> FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR FEJO SJO FEJO SJO
> (ATOMS 75913 75919 75915 75918)
> The atoms refer to iron sulfur cluster present in protein.
> I also added "auto angles dihedrals" to the psfgen script but the result
> didn't change.
> I would appreciate it if anyone can help me with that. If more information
> is required, please just let me know.
>
> Best,
> Kiana
>
>